rectify-rna 2.1.0__tar.gz

rectify_rna-2.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2019-2026 Kevin R. Roy
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

rectify_rna-2.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: rectify-rna
+Version: 2.1.0
+Summary: Unified RNA 3' End Correction Framework for poly(A)-tailed RNA sequencing
+Author-email: "Kevin R. Roy" <kevinrjroy@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/k-roy/RECTIFY
+Project-URL: Bug Tracker, https://github.com/k-roy/RECTIFY/issues
+Project-URL: Publication, https://pubmed.ncbi.nlm.nih.gov/31128237/
+Keywords: RNA,3-prime-end,polyadenylation,RNA-seq,genomics
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pysam>=0.19.0
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: pyBigWig>=0.3.18
+Requires-Dist: biopython>=1.79
+Requires-Dist: tqdm>=4.60.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=3.0.0; extra == "dev"
+Requires-Dist: black>=22.0.0; extra == "dev"
+Requires-Dist: flake8>=4.0.0; extra == "dev"
+Requires-Dist: mypy>=0.950; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=4.5.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=1.0.0; extra == "docs"
+Dynamic: license-file
+
+# RECTIFY: Unified RNA 3' End Correction Framework
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
+[![Implementation Status](https://img.shields.io/badge/status-complete-brightgreen.svg)](https://github.com/k-roy/RECTIFY)
+[![Tests](https://img.shields.io/badge/tests-147%20passing-brightgreen.svg)](tests/)
+
+**RECTIFY** (**R**NA 3' **E**nd **C**orrection **T**ool **I**ntegrating **F**alse-priming and pol**y**(A) ambiguity) is a unified framework for correcting 3' end mapping artifacts in poly(A)-tailed RNA sequencing data.
+
+## Overview
+
+RECTIFY addresses two fundamental problems affecting RNA 3' end mapping:
+
+1. **A-tract Ambiguity (Universal)**: Genomic A-tracts near true 3' ends create positional uncertainty affecting ALL poly(A)-tailed RNA-seq technologies
+2. **Technology-Specific Artifacts**:
+   - **AG mispriming**: Internal priming on A/G-rich regions (oligo-dT methods)
+   - **Poly(A) tail alignment**: Tail bases align to genomic A-tracts creating systematic shifts (when poly(A) is sequenced)
+
+### Key Features
+
+- **Modular correction strategies** that apply based on sequencing technology
+- **Universal A-tract ambiguity detection** for all poly(A)-tailed RNA-seq
+- **AG mispriming screening** (from original RECTIFY, Roy & Chanfreau 2019)
+- **Poly(A) tail trimming and indel artifact correction** (for direct RNA-seq: nanopore, Helicos, QuantSeq)
+- **NET-seq refinement** (optional, technology-independent)
+- **Unified output format** with confidence scores and QC flags
+
+## How It Works
+
+RECTIFY corrects common 3' end mapping artifacts through a series of modular steps:
+
+```
+┌─────────────────────────────────────────────────────────────────────────────┐
+│  EXAMPLE 1: Homopolymer Deletion Artifact (Nanopore)                        │
+│  ═══════════════════════════════════════════════════                        │
+│                                                                             │
+│  True RNA:     5'...GCTAAGCTTAAAAAA-3' + AAAAAAAAAA (poly(A) tail)          │
+│                              └────┘                                         │
+│                         6A genomic tract                                    │
+│                                                                             │
+│  Genome:          ...GCTAAGCTTAAAAAA|GTCACC...     (| = true CPA site)      │
+│                                                                             │
+│  Nanopore read:   ...GCTAAGCTT--AAAA|GTCACC        (2bp deletion in A-tract)│
+│                             ↑↑                                              │
+│                    systematic homopolymer error                             │
+│                                                                             │
+│  Problem:   Aligner maps 3' end 2bp upstream of true position              │
+│             (deletion consumes genomic bases that should be in transcript)  │
+│                                                                             │
+│  RECTIFY:   Detects A-tract deletion, adjusts position +2bp                 │
+│  Result:    Correct 3' end position restored                                │
+└─────────────────────────────────────────────────────────────────────────────┘
+
+┌─────────────────────────────────────────────────────────────────────────────┐
+│  EXAMPLE 2: Multiple Indels Near 3' End                                     │
+│  ═══════════════════════════════════════                                    │
+│                                                                             │
+│  Genome:          ...TACGTTTTTTAAAAAA|GTCA...                               │
+│                          └────┘└────┘                                       │
+│                          T-tract A-tract                                    │
+│                                                                             │
+│  Nanopore read:   ...TACGT---TTAA-AAA|GTCA                                  │
+│                        ↑↑↑     ↑                                            │
+│                   3bp del  1bp del                                          │
+│                                                                             │
+│  RECTIFY logic:                                                             │
+│    • T-tract deletion (3bp): TRUE artifact → correct +3bp                   │
+│    • A-tract deletion (1bp): TRUE artifact → correct +1bp                   │
+│    • Total correction: +4bp                                                 │
+│                                                                             │
+│  Note: Insertions do NOT shift reference coordinates (no correction needed) │
+└─────────────────────────────────────────────────────────────────────────────┘
+
+┌─────────────────────────────────────────────────────────────────────────────┐
+│  EXAMPLE 3: A-tract Ambiguity Window                                        │
+│  ═══════════════════════════════════                                        │
+│                                                                             │
+│  Genome:    ...CGTACAAAAAAAA|GTCACC...                                      │
+│                   └───────┘                                                 │
+│                   8bp A-tract                                               │
+│                                                                             │
+│  Problem:   Any position within the A-tract could be the true 3' end        │
+│             (indistinguishable from poly(A) tail)                           │
+│                                                                             │
+│             ...CGTACAAAAAAAA|     ← could be here                           │
+│             ...CGTACAAAAAAA|A     ← or here                                 │
+│             ...CGTACAAAAAA|AA     ← or here                                 │
+│             ...CGTACAAAAA|AAA     ← etc.                                    │
+│                                                                             │
+│  RECTIFY:   Reports ambiguity window [pos-7, pos] with range=8              │
+│             Confidence score reflects uncertainty                           │
+└─────────────────────────────────────────────────────────────────────────────┘
+
+┌─────────────────────────────────────────────────────────────────────────────┐
+│  EXAMPLE 4: NET-seq Refinement                                              │
+│  ═════════════════════════════                                              │
+│                                                                             │
+│  Genome:    ...CGTACAAAAAAAA|GTCACC...                                      │
+│                   └───────┘                                                 │
+│               ambiguity window                                              │
+│                                                                             │
+│  NET-seq:           ▁▂▃█▇▅▂▁                                                │
+│  signal:               ↑                                                    │
+│                    peak at -3                                               │
+│                                                                             │
+│  RECTIFY:   Uses NET-seq Pol II occupancy to identify most likely           │
+│             termination site within the ambiguity window                    │
+│                                                                             │
+│  Result:    Position refined to NET-seq peak, confidence = HIGH             │
+└─────────────────────────────────────────────────────────────────────────────┘
+
+Pipeline Flow:
+══════════════
+
+  ┌──────────┐    ┌─────────────┐    ┌─────────────┐    ┌─────────────┐
+  │  Input   │    │  Module 1   │    │ Module 2A/B │    │  Module 3   │
+  │   BAM    │───▶│   A-tract   │───▶│  Poly(A) &  │───▶│   NET-seq   │
+  │          │    │  Ambiguity  │    │   Indels    │    │ Refinement  │
+  └──────────┘    └─────────────┘    └─────────────┘    └─────────────┘
+                        │                  │                  │
+                        ▼                  ▼                  ▼
+                  ┌───────────────────────────────────────────────┐
+                  │              Corrected 3' Ends                │
+                  │   (position, ambiguity range, confidence)     │
+                  └───────────────────────────────────────────────┘
+```
+
+## Installation
+
+### From source (development)
+
+```bash
+git clone https://github.com/k-roy/RECTIFY.git
+cd RECTIFY
+pip install -e .
+```
+
+### From PyPI (future release)
+
+```bash
+pip install rectify
+```
+
+## Quick Start
+
+### QuantSeq (oligo-dT short-read)
+
+```bash
+rectify correct quantseq.bam \
+  --genome sacCer3.fa \
+  --annotation genes.gtf \
+  --polya-sequenced \
+  --output corrected_3ends.tsv
+```
+
+### Nanopore direct RNA-seq with NET-seq refinement
+
+```bash
+rectify correct nanopore.bam \
+  --genome sacCer3.fa \
+  --annotation genes.gtf \
+  --polya-sequenced \
+  --aligner minimap2 \
+  --netseq-dir churchman_bigwigs/ \
+  --output corrected_3ends.tsv
+```
+
+## Output Format
+
+RECTIFY produces a TSV file with corrected 3' end positions and QC metrics:
+
+```
+read_id  chrom  strand  raw_position  corrected_position  ambiguity_min  ambiguity_max  ambiguity_range  correction_type  confidence  qc_flags
+read001  chrI   +       147588        147585              147583         147588         5                polya_trim       high        PASS
+read002  chrI   +       147593        147591              147591         147593         2                ag_mispriming    medium      AG_RICH
+```
+
+## Module Architecture
+
+RECTIFY applies corrections modularly based on your data:
+
+1. **Module 1: A-tract Ambiguity** (always applied)
+   - Identifies genomic A-tracts near 3' ends
+   - Calculates ambiguity windows
+
+2. **Module 2A: AG Mispriming** (when oligo-dT priming used)
+   - Screens for downstream AG-richness
+   - Flags likely misprimed reads
+
+3. **Module 2B+2C: Poly(A) Corrections** (when poly(A) IS sequenced)
+   - Models and trims poly(A) tails
+   - Detects and removes indel artifacts
+
+4. **Module 3: NET-seq Refinement** (optional)
+   - Resolves ambiguity using NET-seq data
+   - Assigns confidence scores
+
+## Citation
+
+If you use RECTIFY, please cite:
+
+**Original RECTIFY (AG mispriming correction):**
+> Roy KR, Chanfreau GF. Robust mapping of polyadenylated and non-polyadenylated RNA 3' ends at nucleotide resolution by 3'-end sequencing. *Methods*. 2020 Apr 1;176:4-13. doi: 10.1016/j.ymeth.2019.05.016. [PMID: 31128237](https://pubmed.ncbi.nlm.nih.gov/31128237/)
+
+**RECTIFY 2.0 (unified framework):**
+> Manuscript in preparation
+
+## License
+
+MIT License - See [LICENSE](LICENSE) for details
+
+## Contact
+
+- Kevin R. Roy - [kevinrjroy@gmail.com](mailto:kevinrjroy@gmail.com)
+- GitHub: [k-roy/RECTIFY](https://github.com/k-roy/RECTIFY)
+
+## Acknowledgments
+
+- Original RECTIFY development supported by Chanfreau Lab, UCLA
+- NET-seq data from Churchman Lab, Harvard Medical School

rectify_rna-2.1.0/README.md

@@ -0,0 +1,220 @@
+# RECTIFY: Unified RNA 3' End Correction Framework
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
+[![Implementation Status](https://img.shields.io/badge/status-complete-brightgreen.svg)](https://github.com/k-roy/RECTIFY)
+[![Tests](https://img.shields.io/badge/tests-147%20passing-brightgreen.svg)](tests/)
+
+**RECTIFY** (**R**NA 3' **E**nd **C**orrection **T**ool **I**ntegrating **F**alse-priming and pol**y**(A) ambiguity) is a unified framework for correcting 3' end mapping artifacts in poly(A)-tailed RNA sequencing data.
+
+## Overview
+
+RECTIFY addresses two fundamental problems affecting RNA 3' end mapping:
+
+1. **A-tract Ambiguity (Universal)**: Genomic A-tracts near true 3' ends create positional uncertainty affecting ALL poly(A)-tailed RNA-seq technologies
+2. **Technology-Specific Artifacts**:
+   - **AG mispriming**: Internal priming on A/G-rich regions (oligo-dT methods)
+   - **Poly(A) tail alignment**: Tail bases align to genomic A-tracts creating systematic shifts (when poly(A) is sequenced)
+
+### Key Features
+
+- **Modular correction strategies** that apply based on sequencing technology
+- **Universal A-tract ambiguity detection** for all poly(A)-tailed RNA-seq
+- **AG mispriming screening** (from original RECTIFY, Roy & Chanfreau 2019)
+- **Poly(A) tail trimming and indel artifact correction** (for direct RNA-seq: nanopore, Helicos, QuantSeq)
+- **NET-seq refinement** (optional, technology-independent)
+- **Unified output format** with confidence scores and QC flags
+
+## How It Works
+
+RECTIFY corrects common 3' end mapping artifacts through a series of modular steps:
+
+```
+┌─────────────────────────────────────────────────────────────────────────────┐
+│  EXAMPLE 1: Homopolymer Deletion Artifact (Nanopore)                        │
+│  ═══════════════════════════════════════════════════                        │
+│                                                                             │
+│  True RNA:     5'...GCTAAGCTTAAAAAA-3' + AAAAAAAAAA (poly(A) tail)          │
+│                              └────┘                                         │
+│                         6A genomic tract                                    │
+│                                                                             │
+│  Genome:          ...GCTAAGCTTAAAAAA|GTCACC...     (| = true CPA site)      │
+│                                                                             │
+│  Nanopore read:   ...GCTAAGCTT--AAAA|GTCACC        (2bp deletion in A-tract)│
+│                             ↑↑                                              │
+│                    systematic homopolymer error                             │
+│                                                                             │
+│  Problem:   Aligner maps 3' end 2bp upstream of true position              │
+│             (deletion consumes genomic bases that should be in transcript)  │
+│                                                                             │
+│  RECTIFY:   Detects A-tract deletion, adjusts position +2bp                 │
+│  Result:    Correct 3' end position restored                                │
+└─────────────────────────────────────────────────────────────────────────────┘
+
+┌─────────────────────────────────────────────────────────────────────────────┐
+│  EXAMPLE 2: Multiple Indels Near 3' End                                     │
+│  ═══════════════════════════════════════                                    │
+│                                                                             │
+│  Genome:          ...TACGTTTTTTAAAAAA|GTCA...                               │
+│                          └────┘└────┘                                       │
+│                          T-tract A-tract                                    │
+│                                                                             │
+│  Nanopore read:   ...TACGT---TTAA-AAA|GTCA                                  │
+│                        ↑↑↑     ↑                                            │
+│                   3bp del  1bp del                                          │
+│                                                                             │
+│  RECTIFY logic:                                                             │
+│    • T-tract deletion (3bp): TRUE artifact → correct +3bp                   │
+│    • A-tract deletion (1bp): TRUE artifact → correct +1bp                   │
+│    • Total correction: +4bp                                                 │
+│                                                                             │
+│  Note: Insertions do NOT shift reference coordinates (no correction needed) │
+└─────────────────────────────────────────────────────────────────────────────┘
+
+┌─────────────────────────────────────────────────────────────────────────────┐
+│  EXAMPLE 3: A-tract Ambiguity Window                                        │
+│  ═══════════════════════════════════                                        │
+│                                                                             │
+│  Genome:    ...CGTACAAAAAAAA|GTCACC...                                      │
+│                   └───────┘                                                 │
+│                   8bp A-tract                                               │
+│                                                                             │
+│  Problem:   Any position within the A-tract could be the true 3' end        │
+│             (indistinguishable from poly(A) tail)                           │
+│                                                                             │
+│             ...CGTACAAAAAAAA|     ← could be here                           │
+│             ...CGTACAAAAAAA|A     ← or here                                 │
+│             ...CGTACAAAAAA|AA     ← or here                                 │
+│             ...CGTACAAAAA|AAA     ← etc.                                    │
+│                                                                             │
+│  RECTIFY:   Reports ambiguity window [pos-7, pos] with range=8              │
+│             Confidence score reflects uncertainty                           │
+└─────────────────────────────────────────────────────────────────────────────┘
+
+┌─────────────────────────────────────────────────────────────────────────────┐
+│  EXAMPLE 4: NET-seq Refinement                                              │
+│  ═════════════════════════════                                              │
+│                                                                             │
+│  Genome:    ...CGTACAAAAAAAA|GTCACC...                                      │
+│                   └───────┘                                                 │
+│               ambiguity window                                              │
+│                                                                             │
+│  NET-seq:           ▁▂▃█▇▅▂▁                                                │
+│  signal:               ↑                                                    │
+│                    peak at -3                                               │
+│                                                                             │
+│  RECTIFY:   Uses NET-seq Pol II occupancy to identify most likely           │
+│             termination site within the ambiguity window                    │
+│                                                                             │
+│  Result:    Position refined to NET-seq peak, confidence = HIGH             │
+└─────────────────────────────────────────────────────────────────────────────┘
+
+Pipeline Flow:
+══════════════
+
+  ┌──────────┐    ┌─────────────┐    ┌─────────────┐    ┌─────────────┐
+  │  Input   │    │  Module 1   │    │ Module 2A/B │    │  Module 3   │
+  │   BAM    │───▶│   A-tract   │───▶│  Poly(A) &  │───▶│   NET-seq   │
+  │          │    │  Ambiguity  │    │   Indels    │    │ Refinement  │
+  └──────────┘    └─────────────┘    └─────────────┘    └─────────────┘
+                        │                  │                  │
+                        ▼                  ▼                  ▼
+                  ┌───────────────────────────────────────────────┐
+                  │              Corrected 3' Ends                │
+                  │   (position, ambiguity range, confidence)     │
+                  └───────────────────────────────────────────────┘
+```
+
+## Installation
+
+### From source (development)
+
+```bash
+git clone https://github.com/k-roy/RECTIFY.git
+cd RECTIFY
+pip install -e .
+```
+
+### From PyPI (future release)
+
+```bash
+pip install rectify
+```
+
+## Quick Start
+
+### QuantSeq (oligo-dT short-read)
+
+```bash
+rectify correct quantseq.bam \
+  --genome sacCer3.fa \
+  --annotation genes.gtf \
+  --polya-sequenced \
+  --output corrected_3ends.tsv
+```
+
+### Nanopore direct RNA-seq with NET-seq refinement
+
+```bash
+rectify correct nanopore.bam \
+  --genome sacCer3.fa \
+  --annotation genes.gtf \
+  --polya-sequenced \
+  --aligner minimap2 \
+  --netseq-dir churchman_bigwigs/ \
+  --output corrected_3ends.tsv
+```
+
+## Output Format
+
+RECTIFY produces a TSV file with corrected 3' end positions and QC metrics:
+
+```
+read_id  chrom  strand  raw_position  corrected_position  ambiguity_min  ambiguity_max  ambiguity_range  correction_type  confidence  qc_flags
+read001  chrI   +       147588        147585              147583         147588         5                polya_trim       high        PASS
+read002  chrI   +       147593        147591              147591         147593         2                ag_mispriming    medium      AG_RICH
+```
+
+## Module Architecture
+
+RECTIFY applies corrections modularly based on your data:
+
+1. **Module 1: A-tract Ambiguity** (always applied)
+   - Identifies genomic A-tracts near 3' ends
+   - Calculates ambiguity windows
+
+2. **Module 2A: AG Mispriming** (when oligo-dT priming used)
+   - Screens for downstream AG-richness
+   - Flags likely misprimed reads
+
+3. **Module 2B+2C: Poly(A) Corrections** (when poly(A) IS sequenced)
+   - Models and trims poly(A) tails
+   - Detects and removes indel artifacts
+
+4. **Module 3: NET-seq Refinement** (optional)
+   - Resolves ambiguity using NET-seq data
+   - Assigns confidence scores
+
+## Citation
+
+If you use RECTIFY, please cite:
+
+**Original RECTIFY (AG mispriming correction):**
+> Roy KR, Chanfreau GF. Robust mapping of polyadenylated and non-polyadenylated RNA 3' ends at nucleotide resolution by 3'-end sequencing. *Methods*. 2020 Apr 1;176:4-13. doi: 10.1016/j.ymeth.2019.05.016. [PMID: 31128237](https://pubmed.ncbi.nlm.nih.gov/31128237/)
+
+**RECTIFY 2.0 (unified framework):**
+> Manuscript in preparation
+
+## License
+
+MIT License - See [LICENSE](LICENSE) for details
+
+## Contact
+
+- Kevin R. Roy - [kevinrjroy@gmail.com](mailto:kevinrjroy@gmail.com)
+- GitHub: [k-roy/RECTIFY](https://github.com/k-roy/RECTIFY)
+
+## Acknowledgments
+
+- Original RECTIFY development supported by Chanfreau Lab, UCLA
+- NET-seq data from Churchman Lab, Harvard Medical School

rectify_rna-2.1.0/pyproject.toml

@@ -0,0 +1,78 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "rectify-rna"
+version = "2.1.0"
+description = "Unified RNA 3' End Correction Framework for poly(A)-tailed RNA sequencing"
+authors = [
+    {name = "Kevin R. Roy", email = "kevinrjroy@gmail.com"}
+]
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "MIT"}
+keywords = ["RNA", "3-prime-end", "polyadenylation", "RNA-seq", "genomics"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+dependencies = [
+    "pysam>=0.19.0",
+    "numpy>=1.20.0",
+    "pandas>=1.3.0",
+    "pyBigWig>=0.3.18",
+    "biopython>=1.79",
+    "tqdm>=4.60.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0.0",
+    "pytest-cov>=3.0.0",
+    "black>=22.0.0",
+    "flake8>=4.0.0",
+    "mypy>=0.950",
+]
+docs = [
+    "sphinx>=4.5.0",
+    "sphinx-rtd-theme>=1.0.0",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/k-roy/RECTIFY"
+"Bug Tracker" = "https://github.com/k-roy/RECTIFY/issues"
+"Publication" = "https://pubmed.ncbi.nlm.nih.gov/31128237/"
+
+[project.scripts]
+rectify = "rectify.cli:main"
+
+[tool.setuptools]
+packages = ["rectify", "rectify.core", "rectify.utils"]
+
+[tool.setuptools.package-data]
+rectify = ["data/models/*.json"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_functions = ["test_*"]
+addopts = "-v --cov=rectify --cov-report=html --cov-report=term"
+
+[tool.black]
+line-length = 100
+target-version = ['py38', 'py39', 'py310', 'py311']
+
+[tool.mypy]
+python_version = "3.8"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = false

rectify_rna-2.1.0/rectify/__init__.py

@@ -0,0 +1,36 @@
+"""
+RECTIFY: Unified RNA 3' End Correction Framework
+
+A modular framework for correcting 3' end mapping artifacts in poly(A)-tailed RNA sequencing data.
+
+Modules:
+- A-tract ambiguity detection (universal)
+- AG mispriming screening (oligo-dT methods)
+- Poly(A) tail trimming and indel correction (direct RNA-seq)
+- NET-seq refinement (optional)
+
+Features (v2.1.0):
+- Region-based parallel BAM processing with coverage gap splitting
+- SLURM-aware CPU detection to prevent oversubscription
+- Streaming output mode for large BAM files
+
+Author: Kevin R. Roy
+License: MIT
+"""
+
+__version__ = "2.1.0"
+__author__ = "Kevin R. Roy"
+__email__ = "kevinroy@stanford.edu"
+
+from . import core, utils, slurm
+from .slurm import get_available_cpus, set_thread_limits, is_slurm_job
+
+__all__ = [
+    "core",
+    "utils",
+    "slurm",
+    "get_available_cpus",
+    "set_thread_limits",
+    "is_slurm_job",
+    "__version__",
+]

rectify_rna-2.1.0/rectify/__main__.py

@@ -0,0 +1,9 @@
+#!/usr/bin/env python3
+"""
+Entry point for running RECTIFY as a module: python -m rectify
+"""
+
+from .cli import main
+
+if __name__ == '__main__':
+    main()